My appologies for reposting the final message in this thread. The previous
e-mail sent from a Yahoo mailbox got completely scrubbed ...
----- Forwarded Message -----
From: Boris Vasiliev <bvasil...@yahoo.com>
To: Duncan Mackay <mac...@northnet.com.au>; "gunter.ber...@gene.com"
<gunter.ber...@gene.com>; r-help-r-project.org <r-help@r-project.org>
Sent: Tuesday, February 19, 2013 9:05:17 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and align
x-axes
Duncan and Bert,
Thank you very much for your help with my question. It's very much appreciated.
I used your suggestions to get the plot I needed:
* 3x3 lattice of dotplots,
* x-limits are the same for all panels,
* y-limits and y-ticks in each row are the same,
* y-limits and y-ticks are different between rows,
* within each row subjects are ordered by sum(count) in the row.
My code is below just in case somebody in the r-help list finds it useful.
Regards,
Boris.
# raw data
df <- data.frame(
subject=c('A','A','A',
'BB','BB',
'CCC','CCC','CCC',
'DD','DD',
'A','A','A',
'FFFF','FFFF',
'A','A',
'B','B'),
risk=c('high','high','high',
'high','high',
'high','high','high',
'med','med',
'med','med','med',
'med','med',
'low','low',
'low','low'),
treatment=c('none','optX','optZ',
'none','optZ',
'none','optX','optZ',
'none','optZ',
'none','optX','optZ',
'none','optZ',
'none','optX',
'none','optZ'),
count=c(5,10,2,
3,5,
8,1,2,
3,7,
10,2,5,
15,2,
7,7,
10,8))
# re-level factors
df$risk <- factor(df$risk,levels=c('low','med','high'))
df$treatment <- factor(df$treatment,levels=c('none','optX','optZ'))
# create unique subjects ordered by sum(count) and risk
df$sbj.byrisk <- paste(df$risk,df$subject,sep="_")
df$sbj <- reorder(reorder(df$sbj.byrisk,df$count,sum),as.numeric(df$risk))
df$sbj.ix <- as.numeric(df$sbj)
# for each row (i.e. risk), find limits, ticks, labels, and
# maximum number of points per panel
df.byrisk <- split(df,df['risk'])
ylim <- lapply(df.byrisk,function(idf) return(range(idf$sbj.ix)))
ytck <- lapply(df.byrisk,function(idf) return(sort(unique(idf$sbj.ix))))
ylbl <- lapply(df.byrisk,function(idf) {
ytck <- sort(unique(idf$sbj.ix))
jdnx <- pmatch(ytck,idf$sbj.ix)
ylbl <- sub(".*_","",idf$sbj[jdnx])
return(ylbl)
})
yhei <- unlist(lapply(ytck,length))
# set up lists for limits, ticks, labels, panel heights
ylims <- rep(ylim,c(3,3,3))
ytcks <- rep(list(NULL,NULL,NULL),c(3,3,3))
ytcks[seq(1,7,by=3)] <- ytck
ylbls <- rep(list(NULL,NULL,NULL),c(3,3,3))
ylbls[seq(1,7,by=3)] <- ylbl
# set up plot layout
laywid <- list(axis.panel=c(1,0.1,0.1))
layhei <- list(panel=yhei/sum(yhei))
# plot
oltc <- dotplot(sbj~count|treatment+risk,data=df,
type=c("p","h"),origin=0,
scales=list(x=list(limits=c(-1,16),
alternating=FALSE),
y=list(relation="free",
alternating=FALSE,
limits=ylims,
at=ytcks,
labels=ylbls)),
par.settings=list(layout.widths=laywid,
layout.heights=layhei),
between=list(y=0.2))
useOuterStrips(oltc)
________________________________
From: Duncan Mackay <mac...@northnet.com.au>
To: Boris Vasiliev <bvasil...@yahoo.com>; r-help-r-project.org
<r-help@r-project.org>
Sent: Monday, February 18, 2013 10:29:23 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and align
x-axes
Hi Boris
Just a different take on it, quick glimpse of it
library(lattice)
library(latticeExtra)
z= unique(df$subject)
df$nsub <- sapply(df$subject, pmatch, z)
useOuterStrips(xyplot(count ~ nsub|treatment*risk, df, type = "h", lwd = 2,
scales = list(x = list(at = 1:6, labels = z))))
The order can be changed by changing the order in z by making subject a factor
in the correct order
see
http://finzi.psych.upenn.edu/R/Rhelp02/archive/43626.html
on how to change the yaxis limits. An example of mine (cut and paste) for an
8x3 panel xyplot (it could be streamlined - i needed to change things as I went
along to get everything in)
par.settings = layout.heights = list(panel =
c(1,1,0.6,0.6,0.6,0.6,1,0.5)/sum(c(1,1,0.6,0.6,1,0.6,1,0.5)) )
),
scales = list(x = list(alternating = FALSE,
relation = "same",
rot = 0),
y = list(alternating = FALSE,
relation = "free",
limits =
list(c(-1500,30000),c(-1500,30000),c(-1500,30000), # BZ
c(-1500,30000),c(-1500,30000),c(-1500,30000), # LV
c(-2000,20000),c(-2000,20000),c(-2000,20000), # L2
c( -500, 4000),c( -500,
4000),c( -500, 4000), # CL
c(-2000,20000),c(-2000,20000),c(-2000,20000), # OP
c(-2000,20000),c(-2000,20000),c(-2000,20000), # AB
c(-1500,30000),c(-1500,30000),c(-1500,30000), # MO
c(-500, 4000),c(-500,
4000),c(-500, 4000)), # MX
at = rep(list(seq(0,30000,10000), NULL,
seq(0,30000,10000), NULL,
seq(0,20000,10000), NULL,
seq(0, 4000, 2000), NULL,
seq(0,20000,10000), NULL,
seq(0,20000,10000), NULL,
seq(0,30000,10000), NULL,
seq(0, 4000, 2000), NULL ),
c(1,2, 1,2, 1,2, 1,2, 1,2,
1,2, 1,2, 1,2) ),
labels =
rep(list(as.character(seq(0,30,10)), NULL,
as.character(seq(0,30,10)), NULL,
as.character(seq(0,20,10)), NULL,
as.character(seq(0, 4,
2)), NULL,
as.character(seq(0,20,10)), NULL,
as.character(seq(0,20,10)), NULL,
as.character(seq(0,30,10)), NULL,
as.character(seq(0, 4,
2)), NULL ),
c(1,2, 1,2, 1,2, 1,2,
1,2, 1,2, 1,2, 1,2) ),
rot = 0)
),
I had different panel heights for each row so if they were all the same it
would be
panel = rep(1,n)/n
the trick is to get the rep of the lists to match what would normally happen
for each of the all the panels ie whether an axis/label is required
str(plot object) can help if problems
HTH
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au <mailto:mac...@northnet.com.au>
At 12:22 19/02/2013, you wrote:
> Content-Type: text/plain
> Content-Disposition: inline
> Content-length: 14523
>
> Bert,
>
> Thank you very much for your reply.Ã Your suggestions to set manually
> y-limits of panels in lattice plot certainly puts me on the right track.
>
> It works really well with xyplot():
>
> hf <- data.frame(
> Ã Ã x=seq(1,20,by=1),
> Ã Ã y=seq(0.1,2,by=0.1),
> Ã Ã risk=gl(2,10,labels=c("low","high")),
> Ã Ã treatment=rep(gl(2,5,labels=c("oXX","oYY")),2))Ã Ã Ã Ã Ã Ã Ã Ã
> Ã Ã Ã Ã Ã
> Ã
> xyplot(y~x|treatment+risk,data=hf,type="b",
> Ã Ã Ã Ã Ã Ã scales=list(y=list(limits=list(c(-0.1,1.1),c(-0.1,1.1),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã c(1.0,2.1),c(1.0,2.1)),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> at=list(seq(0,1,0.2),NULL,
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> seq(1,2,0.2),NULL),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã relation="free")))
>
> With the xyplot() above, I get 2x2 lattice where panels in the same row have
> the same y-limits:
>
> Panel 1,2 (row 1): -0.1, 1.1
> Panel 3,4 (row 2): 1.0, 2.1
>
> Unfortunately, it does not work so well with dot plots:
>
>
> kf <- data.frame(subject=c("A","BB","A","C","DDD","DDD"),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> risk=c("low","low","low","high","high","high"),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> treatment=c("oXX","oXX","oYY","oXX","oXX","oYY"),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã count=c(5,7,10,4,13,8))
> kf$risk <- factor(kf$risk,levels=c("low","high"))
> kf$treatment <- factor(kf$treatment,levels=c("oXX","oYY"))
>
> lims.low <- factor(c("A","BB"))
> lims.high <- factor(c("C","DDD"))
> dotplot(subject~count|treatment+risk,data=kf,type=c("p","h"),
> Ã Ã Ã Ã Ã Ã Ã scales=c(y=list(limits=list(lims.low,lims.low,
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> Ã Ã Ã Ã lims.high,lims.high),
> Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã Ã
> relation="free")))
>
>
> With the dotplot() above I get 2x2 lattice plot where all panels haveà the
> same y-limits; y-ticks on all panels are 'A','BB','C','DDD'.
>
>
> This behaviour is probably fixed by design.Ã According to documentation for
> prepanel functions: "... to make this information consistent between panels,
> the ââ¬Ëxlimââ¬â¢ or ââ¬Ëylimââ¬â¢ values should represent all
> the levels of the corresponding factor, even if some are not used within that
> particular panel."
>
> A way to trick lattice would be to use xyplot() with a custom panel
> function.Ã I'll give a try today or tomorrow.
>
> Regards,
> Boris.
>
>
>
>
> ________________________________
> From: Bert Gunter <gunter.ber...@gene.com <mailto:gunter.ber...@gene.com> >
>
> Cc: "mac...@northnet.com.au <mailto:mac...@northnet.com.au> "
> <mac...@northnet.com.au <mailto:mac...@northnet.com.au> >;
> "r-help@r-project.org <mailto:r-help@r-project.org> " <r-help@r-project.org
> <mailto:r-help@r-project.org> >
> Sent: Monday, February 18, 2013 1:09:10 PM
> Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and
> align x-axes
>
> Boris:
>
> If I understand you correctly, you wish to set panel limits by row. I
> know of no "slick" way of doing this (others may), as what is in a row
> can change depending on layout and how you determine the scale for the
> rows' contents may depend on the application context.
>
> So I would do it manually: First, outside of trellis, compute your
> xlim and ylim values for each row as you desire. Then issue the
> trellis call, with the relation="free" component in the scales = list,
> Then just use the list form of the xlim and ylim argument to xyplot
> with your precomputed limits.
>
> -- Bert
>
>
> > Hi Duncan,
> >
> > Thank you for quick reply.
> >
> > I am not sure that your solution solves the problem.Ã If I use
> > useOuterStrips(dotplot(count ~ subject|risk*treatment,df))
> > the order of subjects and panel y-limits in each panel are
> >
> > A, B, BB, CCC, DD, FFFF.
> >
> > However, the order of subjects and y-limits which I would
> > like to get are
> >
> > Panels 1,2,3 (row 1): A, B
> >
> > Panels 4,5,6 (row 2): DD, A, FFFF
> >
> > Panels 7,8,9 (row 3): BB, CCC, A.
> >
> > I can re-index subjects so that they have correct order in each row.
> > However, I am not sure how to specify per-panel y-limits in lattice
> > so that all panels in the same row have the same y-limits irrespective
> > of what data is in these panels.
> >
> > With relation "same", the limits are the same for all plots; with
> > relation "free" the limits depend on the data in the panel.Ã I thought
> > that relation "free" and specification of y-limits via prepanel
> > function (my previous trys) or as a list would do the trick:
> > scales=list(y=list(limits=list(panel-1-limits, panel-2-limits, ...))
> > but I cannot get it to work.
> >
> > I guess I am missing something basic ... any ideas or advice to give
> > up are greatly appreciated.
> >
> > Regards,
> > Boris.
> >
> >
> >
> > Hi Boris
> >
> > Not sure what you mean exactly
> > try
> >
> > library(latticeExtra)
> > useOuterStrips(dotplot(count ~ subject|risk*treatment,df))
> >
> > if you want to change the order of the subjects in each panel and an
> > index column and plot the index column instead of subject and change
> > the scales to suit.
> >
> > HTH
> >
> > Duncan
> >
> > Duncan Mackay
> > Department of Agronomy and Soil Science
> > University of New England
> > Armidale NSW 2351
> > Email: home: mackay at northnet.com.au At 07:54 16/02/2013, you wrote:
> >>Good afternoon, >>I would like to ask for help in controlling y-axis limits
> >>and labels in >lattice doplots.Ã Unfortunately, the problem is somewhat
> >>convoluted, >please bear with the long explanation. >>I would like to
> >>create a 3x3 lattice of dotplots, say subject ~ count. >The plot is
> >>conditioned on variables treatment and risk: subject ~ count >|treatment +
> >>risk.Ã In the experiment,Ã not all subjects were exposed >to all
> >>combinations of treatment and risk.Ã For each risk, I would like >to show
> >>subject ~ count | treatment and order the subjects by the total >count.Ã
> >>At the same time, I would like the x-axes to be the same in all >panels and
> >>aligned by columns. >>Here is a sample data set: >># raw data >df <-
> >>data.frame(subject=c('A','A','A','BB','BB','CCC','CCC','CCC',
> >>>'DD','DD','A','A','A','FFFF','FFFF', >'A','A', 'B','B'),
> >>>>risk=c('high','high','high','high',' high','high','high','high',
> >>>'med','med','med','med','med','med','med',
> >Ã >'low','low','low','low'), >>treatment=c('none
> >','optX','optZ','none','optZ','none','optX','optZ',
> >>>'none','optZ','none','optX','optZ','none','optZ',
> >>'none','optX','none','optZ'), >count=c(5,10,2, 3,5,8,1,2, >3,7,10,2,5,15,2,
> >>7,7,10,8)) ># re-level factors >df$risk <-
> >factor(df$risk,levels=c('low','med','high')) >df $treatment <-
> >factor(df$treatment,levels=c('none','optX','optZ')) >>>## > df >##Ã Ã
> >subject risk treatment count >## 1à à à à A highà à à noneÃ
> >à 5 >## 2à à à à A highà à à optXà à 10 >## 3à à Ã
> >à A highà à à optZà à 2 >## 4à à à BB highà à Ã
> >noneà à 3 >## 5à à à BB highà à à optZà à 5 >## 6à Ã
> >à CCC highà à à noneà à 8 >## 7à à à CCC highà à Ã
> >optXà à 1 >## 8à à à CCC highà à à optZà à 2 >## 9à Ã
> > à DDà medà à à noneà à 3 >## 10à à à DDà medà Ã
> >à optZà à 7 >## 11à à à Aà medà à à noneà à 10 >##
> >12à à à Aà medà à à optXà Ã
> 2 >## 13à à à Aà medà à à optZà à 5 >## 14à à FFFFÃ
> medà à à noneà à 15 >## 15à à FFFFà medà à à optZ
> >à 2 >## 16à à à Aà lowà à à noneà à 7 >## 17à à Ã
> >Aà lowà à à optXà à 7 >## 18à à à Bà lowà à Ã
> >noneà à 10 >## 19à à à Bà lowà à à optZà à 8 >>One way
> >to plot the data is to break-up the data into sub-frames, one >frame for
> >each risk, order subjects by total counts, create dotplots, >and merge with
> >trellis.c().Ã This almost works but in the merged plot I >cannot decrease
> >column spacing to be small enough.Ã Also, the output of >trellis.c() would
> >not work with useOuterStrips() which I really like. >My code is in TRY ONE
> >below. >>Another way to create the plot is specify y-limits for each panel
> >with >custom prepanel and panel functions.Ã For each panel, the data-frame
> >for >the panel row is isolated, subjects in the data-frame for the current
> >>row are ordered by counts, panel y-limits are set to the re-ordered
> >>levels, y-data for each panel is releveled, and data plotted with >standard
> >panel.dotplot().Ã This
> somewhat works but lattice does not >honour
> >Ã the user-defined y-limits and labels are not correct.Ã I suspect >that
> >it is not correct to useà y-relation="same" in this case but "free" >and
> >"sliced" do not give correct results too. My code in in TRY TWO >below. >>If
> >anybody can offer any assistance with this problem, it would be much
> >>appreciated, >Sincerely, >Boris. >>>#### BEGIN TRY ONE - MERGE LATTICE
> >PLOTS #### >library(lattice) >library(latticeExtra) >l ibrary(grid) >>for
> >(irisk in levels(df$risk)) { ># subset data frame >df.irisk <-
> >subset(df,risk==irisk) >># order subjects by total count; store levels of
> >subjectx variables ># for later re-use in panel labels >df.irisk$subjectx <-
> >df.irisk$subject[,drop=TRUE] >df.irisk$subjectx <-
> >reorder(df.irisk$subjectx,df.irisk$count,sum) >a
> >ssign(paste('sbjx.',irisk,sep=''),levels(df.irisk$subjectx)) >># create
> >dotplot and store it in oltc.{irisk} variable >oltc.irisk <-
> >dotplot(subjectx~count|treatment,data=df.irisk,
> >>layout=c(3,1),type=c('p','h'),
> >Ã >xlim=c(-1,16),origin=0, >xlab="",ylab="") >as
> >sign(paste('oltc.',irisk,sep=''),oltc.irisk) >} >># combine everthing in
> >one plot >oltc <- c(low=oltc.low,med=oltc.med,high=oltc.high) >pri nt(oltc)
> >>># get rid of variable labels in middle and right column; decrease >#
> >distance between columns.Ã But can't make inter-column spaces ># small
> >enought and get rid of the panels in all but top rows. >laywid <-
> >trellis.par.get('layout.widths') >laywid$between <- -5 >laywid$axis.panel
> ><- 0.7 >yscales <- list(labels=list(sbjx.low,NULL,NULL, >sbjx.med,N
> >ULL,NULL, >sbjx.high,NULL,NULL)) >oltd <-
> >update(oltc,scales=list(y=yscales), >par.setting
> >s=list(layout.widths=laywid)) >print(oltd) >>### # END TRY ONE - MERGE
> >LATTICE PLOTS #### >>#### BEGIN TRY TWO - CUSTOM PREPANEL AND PANEL
> >FUNCTIONS #### >>prepanel.dotplot.x <-
> >function(x,y,type,subscripts,...,data=NULL) { ># find data-frame that
> >corresponds to the entire row of the plot >irisk <-
> >Ã levels(data$risk[subscripts,drop=TRUE]) >idata <-
> >subset(data,risk==irisk) >># in the sub-frame, order subjects by total
> >counts >idata$subjectx <- reorder(idata$subject[,drop=TRUE],idata$count,sum)
> > >># set y-limits >ylim <- levels(idata$subjectx) >># increment packet
> >counter and print new panel limits >pcknum =
> >lattice.options()$packet.counter >lattice.option s(packet.counter=pcknum+1)
> >>cat(paste(pcknum,":" ,paste(ylim,collapse=", ")),sep="\n")
> >>return(list(ylim=ylim)) >} >>pane l.dotplot.x <-
> >function(x,y,type,subscripts,...,data=NULL) { ># get the sub-frame for the
> >row >irisk <- levels(data$risk[subscripts,drop=TRUE]) >idata <-
> >subset(data,risk==irisk) >># in the sub-frame, order subjects by total
> >counts >idata$subjectx <- reorder(idata$subject[,drop=TRUE],idata$count,sum)
> > >># re-order y-variable to "correct levels" >y <-
> >factor(as.character(y),levels(idata$subjectx)) > ># print levels of the
> >releveled subjects - should be the same ># as the output of
> >Ã prepanel.dotplot.x >pnlnum <- panel.number()
> >>cat(paste(pnlnum,':',paste(level s(y),collapse=", ")),sep="\n") >># call
> >standard dotplot >panel.dotplot(x,y,...) >} >># the data is plotted
> >correctly but the labels and limits are not >correct
> >>lattice.options(packet.counter=1) >oltc <-
> >dotplot(subject~count|treatment+risk,data=df, >l
> >ayout=c(3,3),subscripts=TRUE, >prepanel=function (...)
> >>{prepanel.dotplot.x(...,data=df)}, >panel
> >=function(...){panel.dotplot.x(...,data=df)}, >s
> >cales=list(y=list(relation='same')), >drop.unuse d.levels=FALSE,
> >>xlim=c(0,16)) >print(oltc) >>## ## END TRY TWO - CUSTOM PANEL AND PREPANEL
> >FUNCTIONS #### >>_________________________________________ _____ >R-help at
> >r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-he lp
> >>PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html >and provide commented,
> >minimal, self-contained, reproducible code.
> >Ã Ã Ã Ã [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org <mailto:R-help@r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
> [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help@r-project.org <mailto:R-help@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
